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Structural investigation, computational analysis, and theoretical cryoprotectant approach of antifreeze protein type IV mutants

Antifreeze proteins (AFPs) have unique features to sustain life in sub-zero environments due to ice recrystallization inhibition (IRI) and thermal hysteresis (TH). AFPs are in demand as agents in cryopreservation, but some antifreeze proteins have low levels of activity. This research aims to improv...

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Main Authors: Eskandari, Azadeh, Leow, Thean Chor, Abdul Rahman, Mohd Basyaruddin, Oslan, Siti Nurbaya
Format: Article
Published: Springer Science and Business Media Deutschland GmbH 2024
Online Access:http://psasir.upm.edu.my/id/eprint/114650/
https://link.springer.com/article/10.1007/s00249-024-01719-7?error=cookies_not_supported&code=61929831-03f6-4180-a37f-653165443dc6
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spelling my.upm.eprints.1146502025-01-22T02:34:54Z http://psasir.upm.edu.my/id/eprint/114650/ Structural investigation, computational analysis, and theoretical cryoprotectant approach of antifreeze protein type IV mutants Eskandari, Azadeh Leow, Thean Chor Abdul Rahman, Mohd Basyaruddin Oslan, Siti Nurbaya Antifreeze proteins (AFPs) have unique features to sustain life in sub-zero environments due to ice recrystallization inhibition (IRI) and thermal hysteresis (TH). AFPs are in demand as agents in cryopreservation, but some antifreeze proteins have low levels of activity. This research aims to improve the cryopreservation activity of an AFPIV. In this in silico study, the helical peptide afp1m from an Antarctic yeast AFP was modeled into a sculpin AFPIV, to replace each of its four α-helices in turn, using various computational tools. Additionally, a new linker between the first two helices of AFPIV was designed, based on a flounder AFPI, to boost the ice interaction activity of the mutants. Bioinformatics tools such as ExPASy Prot-Param, Pep-Wheel, SOPMA, GOR IV, Swiss-Model, Phyre2, MODFOLD, MolPropity, and ProQ were used to validate and analyze the structural and functional properties of the model proteins. Furthermore, to evaluate the AFP/ice interaction, molecular dynamics (MD) simulations were executed for 20, 100, and 500 ns at various temperatures using GROMACS software. The primary, secondary, and 3D modeling analysis showed the best model for a redesigned antifreeze protein (AFP1mb, with afp1m in place of the fourth AFPIV helix) with a QMEAN (Swiss-Model) Z score value of 0.36, a confidence of 99.5%, a coverage score of 22%, and a p value of 0.01. The results of the MD simulations illustrated that AFP1mb had more rigidity and better ice interactions as a potential cryoprotectant than the other models; it also displayed enhanced activity in limiting ice growth at different temperatures. Springer Science and Business Media Deutschland GmbH 2024-09-27 Article PeerReviewed Eskandari, Azadeh and Leow, Thean Chor and Abdul Rahman, Mohd Basyaruddin and Oslan, Siti Nurbaya (2024) Structural investigation, computational analysis, and theoretical cryoprotectant approach of antifreeze protein type IV mutants. European Biophysics Journal, 53. pp. 385-403. ISSN 0175-7571; eISSN: 1432-1017 https://link.springer.com/article/10.1007/s00249-024-01719-7?error=cookies_not_supported&code=61929831-03f6-4180-a37f-653165443dc6 10.1007/s00249-024-01719-7
institution Universiti Putra Malaysia
building UPM Library
collection Institutional Repository
continent Asia
country Malaysia
content_provider Universiti Putra Malaysia
content_source UPM Institutional Repository
url_provider http://psasir.upm.edu.my/
description Antifreeze proteins (AFPs) have unique features to sustain life in sub-zero environments due to ice recrystallization inhibition (IRI) and thermal hysteresis (TH). AFPs are in demand as agents in cryopreservation, but some antifreeze proteins have low levels of activity. This research aims to improve the cryopreservation activity of an AFPIV. In this in silico study, the helical peptide afp1m from an Antarctic yeast AFP was modeled into a sculpin AFPIV, to replace each of its four α-helices in turn, using various computational tools. Additionally, a new linker between the first two helices of AFPIV was designed, based on a flounder AFPI, to boost the ice interaction activity of the mutants. Bioinformatics tools such as ExPASy Prot-Param, Pep-Wheel, SOPMA, GOR IV, Swiss-Model, Phyre2, MODFOLD, MolPropity, and ProQ were used to validate and analyze the structural and functional properties of the model proteins. Furthermore, to evaluate the AFP/ice interaction, molecular dynamics (MD) simulations were executed for 20, 100, and 500 ns at various temperatures using GROMACS software. The primary, secondary, and 3D modeling analysis showed the best model for a redesigned antifreeze protein (AFP1mb, with afp1m in place of the fourth AFPIV helix) with a QMEAN (Swiss-Model) Z score value of 0.36, a confidence of 99.5%, a coverage score of 22%, and a p value of 0.01. The results of the MD simulations illustrated that AFP1mb had more rigidity and better ice interactions as a potential cryoprotectant than the other models; it also displayed enhanced activity in limiting ice growth at different temperatures.
format Article
author Eskandari, Azadeh
Leow, Thean Chor
Abdul Rahman, Mohd Basyaruddin
Oslan, Siti Nurbaya
spellingShingle Eskandari, Azadeh
Leow, Thean Chor
Abdul Rahman, Mohd Basyaruddin
Oslan, Siti Nurbaya
Structural investigation, computational analysis, and theoretical cryoprotectant approach of antifreeze protein type IV mutants
author_facet Eskandari, Azadeh
Leow, Thean Chor
Abdul Rahman, Mohd Basyaruddin
Oslan, Siti Nurbaya
author_sort Eskandari, Azadeh
title Structural investigation, computational analysis, and theoretical cryoprotectant approach of antifreeze protein type IV mutants
title_short Structural investigation, computational analysis, and theoretical cryoprotectant approach of antifreeze protein type IV mutants
title_full Structural investigation, computational analysis, and theoretical cryoprotectant approach of antifreeze protein type IV mutants
title_fullStr Structural investigation, computational analysis, and theoretical cryoprotectant approach of antifreeze protein type IV mutants
title_full_unstemmed Structural investigation, computational analysis, and theoretical cryoprotectant approach of antifreeze protein type IV mutants
title_sort structural investigation, computational analysis, and theoretical cryoprotectant approach of antifreeze protein type iv mutants
publisher Springer Science and Business Media Deutschland GmbH
publishDate 2024
url http://psasir.upm.edu.my/id/eprint/114650/
https://link.springer.com/article/10.1007/s00249-024-01719-7?error=cookies_not_supported&code=61929831-03f6-4180-a37f-653165443dc6
_version_ 1823093219907338240
score 13.244413

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